Python@3.11 fails to install in GitHub runner image #173191

bebound · 2024-05-30T03:27:00Z

`brew gist-logs <formula>` link OR `brew config` AND `brew doctor` output

HOMEBREW_VERSION: 4.3.2
ORIGIN: https://github.com/Homebrew/brew
HEAD: 9fdb0d53990d3e62e25325a6f89dbb769e84a530
Last commit: 3 days ago
Core tap HEAD: d9c1c710da2bc80ab6f41c57af1b6ba622fc7686
Core tap last commit: 4 minutes ago
Core tap JSON: 30 May 03:00 UTC
Core cask tap HEAD: 653ebda172de4be72eba8b018ae5b89fde67aca3
Core cask tap last commit: 2 hours ago
Core cask tap JSON: 30 May 03:00 UTC
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: ["--no-quarantine"]
HOMEBREW_COLOR: set
HOMEBREW_MAKE_JOBS: 4
HOMEBREW_NO_AUTO_UPDATE: set
HOMEBREW_NO_INSTALL_CLEANUP: set
Homebrew Ruby: 3.3.1 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/3.3.1/bin/ruby
CPU: quad-core 64-bit ivybridge
Clang: 14.0.0 build 1400
Git: 2.45.1 => /usr/local/bin/git
Curl: 8.4.0 => /usr/bin/curl
macOS: 12.7.4-x86_64
CLT: 14.2.0.0.1.1668646533
Xcode: 14.2 => /Applications/Xcode_14.2.app/Contents/Developer


Please note that these warnings are just used to help the Homebrew maintainers
Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  openssl@1.1
  packer
  ruby@3.0

with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed formulae are deprecated or disabled.
You should find replacements for the following formulae:
  openssl@1.1
  packer
  ruby@3.0

Warning: You have an unnecessary local Cask tap.
This can cause problems installing up-to-date casks.
Please remove it by running:
  brew untap homebrew/cask

Warning: You have an unnecessary local Cask tap.
This can cause problems installing up-to-date casks.
Please remove it by running:
  brew untap homebrew/cask

Warning: You have an unnecessary local Core tap!
This can cause problems installing up-to-date formulae.
Please remove it by running:
 brew untap homebrew/core

Warning: You have an unnecessary local Core tap!
This can cause problems installing up-to-date formulae.
Please remove it by running:
 brew untap homebrew/core

Warning: Broken symlinks were found. Remove them with `brew cleanup`:
  /usr/local/etc/bash_completion.d/prlctl
  /usr/local/etc/bash_completion.d/prlsrvctl
  /usr/local/share/man/man8/prl_convert.8
  /usr/local/share/man/man8/prl_disk_tool.8
  /usr/local/share/man/man8/prlctl.8
  /usr/local/share/man/man8/prlexec.8
  /usr/local/share/man/man8/prlsrvctl.8

Warning: Broken symlinks were found. Remove them with `brew cleanup`:
  /usr/local/etc/bash_completion.d/prlctl
  /usr/local/etc/bash_completion.d/prlsrvctl
  /usr/local/share/man/man8/prl_convert.8
  /usr/local/share/man/man8/prl_disk_tool.8
  /usr/local/share/man/man8/prlctl.8
  /usr/local/share/man/man8/prlexec.8
  /usr/local/share/man/man8/prlsrvctl.8

Verification

My brew doctor output says Your system is ready to brew. and am still able to reproduce my issue.
I ran brew update and am still able to reproduce my issue.
I have resolved all warnings from brew doctor and that did not fix my problem.
I searched for recent similar issues at https://github.com/Homebrew/homebrew-core/issues?q=is%3Aissue and found no duplicates.

What were you trying to do (and why)?

Install Python@3.11 package

Related issue: Azure/azure-cli#29054

What happened (include all command output)?

The exit code is 1

Run brew install python@3.11
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.11/manifests/3.11.9
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/434092e38cddf8d8908f3dad7a233fe43e47dc9fdf39bac5845e656f0bc1110f--python@3.11-3.11.9.bottle_manifest.json
==> Fetching python@3.11
==> Downloading https://ghcr.io/v2/homebrew/core/python/3.11/blobs/sha256:35a3fa7bc0dd78055d3ff8ca238366d7c78bb322cd5c09d8a2f3b4e7d07baf82
Already downloaded: /Users/runner/Library/Caches/Homebrew/downloads/a0eeb298568552038d4e047fd56d4c8be093bb55336e93047b56e783268a5d86--python@3.11--3.11.9.monterey.bottle.tar.gz
==> Pouring python@3.11--3.11.9.monterey.bottle.tar.gz
Error: The `brew link` step did not complete successfully
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/2to3-3.11
Target /usr/local/bin/2to3-3.11
already exists. You may want to remove it:
  rm '/usr/local/bin/2to3-3.11'

To force the link and overwrite all conflicting files:
  brew link --overwrite python@3.11

To list all files that would be deleted:
  brew link --overwrite python@3.11 --dry-run

Possible conflicting files are:
/usr/local/bin/2to3-3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/2to3-3.11
/usr/local/bin/idle3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/idle3.11
/usr/local/bin/pydoc3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/pydoc3.11
/usr/local/bin/python3.11 -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11
/usr/local/bin/python3.11-config -> /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11-config
==> /usr/local/Cellar/python@3.11/3.11.9/bin/python3.11 -Im ensurepip
==> /usr/local/Cellar/python@3.11/3.11.9/bin/python3.11 -Im pip install -v --no-
==> Caveats
Python has been installed as
  /usr/local/bin/python3.11

Unversioned and major-versioned symlinks `python`, `python3`, `python-config`, `python3-config`, `pip`, `pip3`, etc. pointing to
`python3.11`, `python3.11-config`, `pip3.11` etc., respectively, have been installed into
  /usr/local/opt/python@3.11/libexec/bin

You can install Python packages with
  pip3.11 install <package>
They will install into the site-package directory
  /usr/local/lib/python3.11/site-packages

tkinter is no longer included with this formula, but it is available separately:
  brew install python-tk@3.11

gdbm (`dbm.gnu`) is no longer included in this formula, but it is available separately:
  brew install python-gdbm@3.11
`dbm.ndbm` changed database backends in Homebrew Python 3.11.
If you need to read a database from a previous Homebrew Python created via `dbm.ndbm`,
you'll need to read your database using the older version of Homebrew Python and convert to another format.
`dbm` still defaults to `dbm.gnu` when it is installed.

If you do not need a specific version of Python, and always want Homebrew's `python3` in your PATH:
  brew install python3

For more information about Homebrew and Python, see: https://docs.brew.sh/Homebrew-and-Python
==> Summary
🍺  /usr/local/Cellar/python@3.11/3.11.9: 3,327 files, 62.3MB
Error: Process completed with exit code 1.

What did you expect to happen?

The exit code should be 0

Step-by-step reproduction instructions (by running `brew` commands)

Here is the command:

brew update
brew uninstall azure-cli
brew install python@3.11

Here is the GitHub workflow log:
https://github.com/bebound/starter-workflows/actions/runs/9296281295/job/25584574480

The text was updated successfully, but these errors were encountered:

bebound · 2024-05-30T03:29:59Z

This could be fixed by running brew unlink python@3.11 && brew link --overwrite python@3.11 at the beginning.

This is treated as a runner image bug in #165793 (comment) when installing python@3.12
However, it's also treated it as a Homebrew bug in actions/runner-images#9471 (comment)

I wonder what's the real cause of this issue.

carlocab · 2024-05-30T03:53:41Z

Could you check what the output of

file /usr/local/bin/2to3-3.11
ls -la /usr/local/bin/2to3-3.11
readlink /usr/local/bin/2to3-3.11

is before doing brew install python@3.11?

Bo98 · 2024-05-30T04:08:19Z

I wonder what's the real cause of this issue.

The real cause is GitHub Actions installs non-Homebrew Python into the Homebrew prefix so it's a GitHub bug due to that since you can't install two things into the same place.

The issue is fixed on their macos-14 image. It will likely never be fixed on their older images at this point.

carlocab · 2024-05-30T05:03:41Z

The real cause is GitHub Actions installs non-Homebrew Python into the Homebrew prefix so it's a GitHub bug due to that since you can't install two things into the same place.

This was my suspicion too, but wanted to be sure. No idea why actions/runner-images#9471 (comment) suggests otherwise.

bebound · 2024-05-30T05:11:48Z

Could you check what the output of
file /usr/local/bin/2to3-3.11
ls -la /usr/local/bin/2to3-3.11
readlink /usr/local/bin/2to3-3.11 
is before doing brew install python@3.11?

Run file /usr/local/bin/2to3-3.11
/usr/local/bin/2to3-3.11: a /Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11 script text executable, ASCII text

Run ls -la /usr/local/bin/2to3-3.11
lrwxr-xr-x  1 root  wheel  72 May 15 02:33 /usr/local/bin/2to3-3.11 -> ../../../Library/Frameworks/Python.framework/Versions/3.11/bin/2to3-3.11

Run readlink /usr/local/bin/2to3-3.11
../../../Library/Frameworks/Python.framework/Versions/3.11/bin/2to3-3.11

carlocab · 2024-05-30T06:40:02Z

Yep, seems like a GitHub Actions issue to me.

Try doing

brew install --overwrite python@3.11

bebound · 2024-05-30T07:31:51Z

brew install --overwrite python@3.11 also works.

It appears that the link file generated by /Library/Frameworks/Python.framework/Versions/3.11/ conflict with python@3.11.

I believe this is a runner image bug, I'll create a bug report later.

Ref:
actions/setup-python#577
actions/runner-images#7710

Bo98 · 2024-05-30T11:48:00Z

They did fix it in the past for 2.7: https://github.com/actions/runner-images/blob/9d5d1be4828f3f7e54796a46d60afd0a2f9e05b0/images/macos/scripts/build/install-python.sh#L17-L25

but never fixed 3.x: https://github.com/actions/python-versions/blob/c990e6da9586f6b33bf19aba61c934ded6ec28c5/installers/macos-pkg-setup-template.sh#L42

Workaround for Homebrew/homebrew-core#173191

Workaround for github/brew problem. Python is already install on the Github action runner and then homebrew comes along... See also: Homebrew/homebrew-core#173191

github-actions · 2024-06-22T00:10:54Z

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs.

bebound added the bug Reproducible Homebrew/homebrew-core bug label May 30, 2024

bebound changed the title ~~Python@3.11 fails to install on GitHub runner image~~ Python@3.11 fails to install in GitHub runner image May 30, 2024

bebound mentioned this issue May 31, 2024

Pre-installed Python conflicts with Homebrew Python on macOS actions/runner-images#9966

Open

14 tasks

fxcoudert added the upstream issue An upstream issue report is needed label May 31, 2024

jschwartzentruber added a commit to MozillaSecurity/orion that referenced this issue Jun 5, 2024

Force overwrite of Python 3.11/3.12 symlinks

d2543a5

Workaround for Homebrew/homebrew-core#173191

jschwartzentruber added a commit to MozillaSecurity/orion that referenced this issue Jun 6, 2024

Force overwrite of Python 3.11/3.12 symlinks

1f38a80

Workaround for Homebrew/homebrew-core#173191

jschwartzentruber added a commit to MozillaSecurity/orion that referenced this issue Jun 6, 2024

Force overwrite of Python 3.11/3.12 symlinks

2833ced

Workaround for Homebrew/homebrew-core#173191

joto added a commit to joto/osm2pgsql that referenced this issue Jun 15, 2024

Remove python before brew install

ee09a9d

Workaround for github/brew problem. Python is already install on the Github action runner and then homebrew comes along... See also: Homebrew/homebrew-core#173191

joto mentioned this issue Jun 15, 2024

Remove python before brew install osm2pgsql-dev/osm2pgsql#2201

Merged

joto added a commit to joto/osm2pgsql that referenced this issue Jun 15, 2024

Remove python before brew install

fc85ae2

Workaround for github/brew problem. Python is already install on the Github action runner and then homebrew comes along... See also: Homebrew/homebrew-core#173191

github-actions bot added the stale No recent activity label Jun 22, 2024

github-actions bot closed this as not planned Won't fix, can't repro, duplicate, stale Jun 29, 2024

rushilmehra mentioned this issue Jul 23, 2024

(ci): Fix macos crossbuild action by forcing brew link w python@3.11 cloudflare/boring#250

Merged

rfomin mentioned this issue Oct 7, 2024

Add macos artifact uploading kraflab/dsda-doom#513

Merged

kahest mentioned this issue Nov 29, 2024

fix: symlink error for cask python 3.11 on macos-13 getsentry/apple-system-symbols-upload#35

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Python@3.11 fails to install in GitHub runner image #173191

Python@3.11 fails to install in GitHub runner image #173191

bebound commented May 30, 2024 •

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Bo98 commented May 30, 2024 •

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github-actions bot commented Jun 22, 2024

Python@3.11 fails to install in GitHub runner image #173191

Python@3.11 fails to install in GitHub runner image #173191

Comments

bebound commented May 30, 2024 • edited Loading

brew gist-logs <formula> link OR brew config AND brew doctor output

Verification

What were you trying to do (and why)?

What happened (include all command output)?

What did you expect to happen?

Step-by-step reproduction instructions (by running brew commands)

bebound commented May 30, 2024 • edited Loading

carlocab commented May 30, 2024 • edited Loading

Bo98 commented May 30, 2024 • edited Loading

carlocab commented May 30, 2024

bebound commented May 30, 2024 • edited Loading

carlocab commented May 30, 2024

bebound commented May 30, 2024 • edited Loading

Bo98 commented May 30, 2024 • edited Loading

github-actions bot commented Jun 22, 2024

bebound commented May 30, 2024 •

edited

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`brew gist-logs <formula>` link OR `brew config` AND `brew doctor` output

Step-by-step reproduction instructions (by running `brew` commands)

bebound commented May 30, 2024 •

edited

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carlocab commented May 30, 2024 •

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Bo98 commented May 30, 2024 •

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bebound commented May 30, 2024 •

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bebound commented May 30, 2024 •

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Bo98 commented May 30, 2024 •

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